


Not Just Pheromones

by Hyx_Sydin



Category: Stargate Atlantis
Genre: Alpha/Beta/Omega Dynamics, Alternate Universe - No Stargate, Knotting, M/M, Mates, Mildly Dubious Consent, Riding
Language: English
Status: In-Progress
Published: 2014-09-22
Updated: 2014-09-27
Packaged: 2018-02-18 08:22:42
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 2
Words: 4,727
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2341565
Author URL: https://archiveofourown.org/users/Hyx_Sydin/pseuds/Hyx_Sydin
Summary: <blockquote class="userstuff">
              <p>Rodney McKay has worked hard to build his empire, both legally and illegally, which has left little time for personal pursuits; not that he can indulge in those openly anyway. And then one night he meets John, who shows an interest in him, and Rodney can't help but want him.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> The original idea was pure smut :D and instead it became this when I wrote it - I don't even know what this is to be honest, or if the tags are correct/enough :?
> 
> I have no beta so there may be errors, especially since I didn't give it a read after writing it...

Rodney McKay stood at the windows of his ‘other’ office watching as the newest shipment was unloaded, examined and then catalogued before being taken to the three different holding cells dependent on their nature. 

At the moment, his CMO was examining an elderly woman as his aide, Marie something or other, entered whatever information was pertinent into the stock database. When the doctor completed his task, the two security officers assigned to the woman moved her to the next station for cataloguing, and the next person was unloaded from the truck.

The change in his security personnel; all of them Alphas who now stood taller and more alert, had him stepping closer to the glass for a better look in time to see a very handsome young man climb out of the truck. He had a shock of black hair that stood in every direction and vibrant green eyes and for a moment he thought the young man was an Omega in heat, but instead of the preening the Alphas would have done if such was the case, the Alphas were trying to assert their dominance, as evidenced by the head of his security stepping out of his little office, hand on his weapon, to escort him over to the medical station.

“Ronon,” he said as he activated the radio in his ear, “anything I should know?” but the only response he received was a grunt. 

Knowing better than to disturb Carson while he worked, he made his way to his desk and picked up his tablet, signing into it as he made his way back to the window. A glance out into the warehouse showed Carson entering information into the database himself, his aide nowhere to be seen. It was but a moment’s work before he had access to the device in the doctor’s hand and quickly read through the notes entered so far.

_Young (20 – 25 years old) – Pure-bred Alpha – unconsciously radiates dominance and authority demanding submission – suggest full medical examination in private facility._

Rodney’s brows furrowed in annoyance as he wondered at Carson’s reasoning, until he noticed what was written in the ‘Notes’ section:  
 _He’s more trouble than he’s worth Rodney! I suggest you tranq him and have him dumped somewhere far away and hope it’s the last we see of him. CB_

Turning his back to the window he activated his radio as he made his way to his desk and demanded that Ronon bring the young Alpha to him. When Ronon, the Alpha and three of his security officers arrived, he was glad to be sitting as the young man’s potent cocktail of pheromones filled every corner of his office. Unhappy with the way they made him feel, he chased away the rest of the escorts as Ronon made himself comfortable in one of the many armchairs while the Alpha stood placidly in the center of the room.

After silently watching the other man as he examined his office Rodney spoke, “What is your name?”

Those green eyes snapped to his, and Rodney had to force himself to maintain eye contact and not lower his in obeisance, and after a moment the other answered, “John.”

“That has to be the most common name in the world,” Rodney sighed as he stood and made his way around the desk, “How did you end up in one of my trucks?”

Something flashed across his eyes too quickly for Rodney to read as he looked away, “Plain ol’ dumb luck.”

“I don’t believe in luck,” Rodney said as he pursed his lips, watching the Alpha fidget, “You’re not the kind my men usually bring in, you look like you actually belong somewhere.”

When the only response he received was a shrug, he continued with his questioning, “If I were to release you, would you give me your word that you will forget all that you’ve seen?”

“No,” John’s eyes caught his once again as he answered and Rodney felt the weight of his dominance in his stare.

Taking a step forward in defiance he demanded, “And why not? What is it that you want John?”

“Coming in here and discovering that you are a Beta, I wondered why it is that the Alphas are so loyal, and now I see it,” John said as his mouth twitched up into a smile, “you’re quite formidable in your own right.”

“If you do not answer me,” Rodney growled as he advanced on the Alpha, “I will have Ronon hold you down and inject you with something that will _make_ you answer!”

John held his hands up in a placating manner, which only angered the Beta more, “I don’t really want anything.”

“Then why won’t you give me your word that you will forget this should I release you?”

“Oh that,” John rubbed at the back of his neck as he glanced at the ground, “it’s nothing bad really. Unless- unless it is in your opinion, which would make it like really bad, fatal even . . . for me…”

Rodney’s anger was replaced with confusion as he stared at the Alpha, who now seemed that much younger, “What are you on about?” but as he spoke he became aware of Ronon chuckling and turned to glare at him, “What?”

Darting a glance from one Alpha to the other; John was now blushing while Ronon’s chuckles had turned into full-blown laughter, Rodney took a deep breathe with which to yell with when he noticed it; John was no longer radiating dominance but arousal. Oh.

Turning back to John, whose cheeks were now a bright red, he found himself asking, “Is it that I’m not an Omega?”

“What- no!” John answered as his brows furrowed, peering at Rodney strangely, “Why would you ask that?”

“There are Alphas in this world who abhor Omega companions, who prefer Betas and sometimes even Alphas; I merely wished to know if you were one of them.”

John shook his head, looking uncomfortable as he mumbled, “It doesn’t have anything to do with the fact that you’re a Beta.”

“Oh,” Rodney said curiously, “then what is it then?”

“I’d rather not talk about it,” John said as his blush returned, “Look, if I give you my word, will you let me go?”

“Let me think about it,” Rodney murmured distractedly as he made his way back to his desk and sat down, turning an assessing eye on the young man before him. After a few minutes of watching the Alpha fidget under his gaze, and weighing the pros against the cons, he turned to address Ronon, “I want you to take him to my home Ronon; I will send instructions to Miko on what I want done with him, and I would prefer it if you stayed the night just in case.”

John spluttered in protest as he spoke while Ronon regarded him with a raised eyebrow and the ghost of a smirk before rising out of his seat, “You’re the boss.”

“Yes I am,” Rodney said as he leaned back smugly in his chair as he watched the tall Alpha grab John by the shoulder as he made to launch himself at him and then drag the younger Alpha out, “if you see Teyla, send her up.”

Ronon gave him a thumbs up as he herded the protesting young man out of his office.

\---

Walking into his bedroom Rodney couldn’t help but smile at the image he is presented with; John lie spread-eagled, ankles and wrists tied to the bed’s posts, completely naked. He wasn’t entirely sure how Miko had managed it, but he was glad that she had and would compensate her for it. Picking up the remote control she had placed near the door, he moved to stand at the foot of the bed.

“Hello John,” he said loudly over the other’s sounds of distress causing cloudy green eyes to turn slowly to look at him; when the other man finally recognised him he let out a slow moan as his body arched towards Rodney. 

Annoyed with both himself and Miko for leaving John like this for too long, he used the remote control to stop the air conditioner pumping Omega heat pheromones into the room. He then made his way to the desk in the corner of the room to retrieve a vial of Alpha scent, which he waved under John’s nose. When John began growling and snarling, he stoppered the vial and returned it to the secret drawer in his desk.

“I can’t really have a conversation with you when you’re so completely out of your mind with lust John,” he said conversationally as he made his way back to the bed and found the Alpha blinking up at him as his eyes cleared, “Good, you’re coming round.”

“Bastard,” John growled as he tugged at his restraints, glaring at Rodney.

“It’s really your own fault John, if you had not shown an interest in me you would be waking up in a field somewhere, slightly groggy but completely safe. Not that you’re not safe here,” Rodney said as his eyes trailed down the Alpha’s naked body which was covered in a sheen of sweat, eyes lingering on his impressive erection and developing knot, “it’s just a different kind of safe.”

John eyes were narrowed as he demanded, “Whaddya want?” 

“Oh I want lots of things,” he responded grinning as he undid the belt of his gown and slipped it off to reveal his own nakedness, “but right now? I want you!”

“Did you like the pheromones,” Rodney asked as he put a knee onto the bed, leaned forward onto his knuckles and crawled up John’s body, “they’re my very own.” John’s eyes widened as Rodney kneeled over his groin, reached down to hold his cock in place and then impaled himself causing them both to moan. When Rodney could breathe again he explained, “You can’t do anything in this world as an Omega; so I created myself a Beta scent, moved to another country and created myself an empire.”

“And none,” John panted out as he pulled at his restraints again, hips bucking against Rodney’s weight, “none of the Alphas . . . that work for you . . . they don’t know?”

Rodney smiled as he made himself comfortable, ignoring his body’s demands to have the Alpha’s knot buried in him, “I’ve allowed myself six confidantes, all of them Alphas; my sister Jeannie who I brought with me when I left Canada, the doctor you met at the warehouse, the tall guy with the braids, Radek Zelenka who runs my labs, and lastly Teyla Emmagan and Elizabeth Weir who both help me run my business.”

John’s upper body pushed up off the bed as much as it could as he snarled at Rodney, “What do you want from me?”

A flicker of nervousness settled in his stomach as Rodney answered, “I’m giving you a choice; you can either become my mate or die after I’ve taken my pleasure.”

“Your mate?” the Alpha questioned as he dropped down, face contorted in his confusion, “Why trust me, _want me_ , as your mate?”

“You smell,” Rodney murmured as he leaned forward to sniff under John’s jaw, changing the angle of their body’s joining and drawing out a whimper from the Alpha, as he once again tried to buck up. A tremble ran through Rodney as he ground down involuntarily, gasping as he breathed in the scent of the Alpha beneath him, “you smell powerful and dominant. Can you imagine what it would be like walking into a room full of my rivals with you by my side, as my mate? They will cower before us and before you know it, I’ll be running everything on this Coast!”

John tugged his hands again as he tried to dislodge Rodney, “If that’s what you want, why not recreate yourself as a powerful Alpha?”

“Stop that!” Rodney said as he pinned John’s shoulders to the bed, making an annoyed sound at the back of his throat, “I am well-known as a Beta, and too established here to want to move again. No, it would be better with you at my side.” Lifting up, Rodney looked down into green eyes, “You can be happy here with me; I will give you anything you want, everything you want, as long as you keep my secret.”

John stared at him as he asked, “And what if I want cubs? What if I want _you_ to give me cubs?”

Rodney was genuinely surprised, “You would want cubs with me?”

“I would want cubs with my mate,” John stated matter-of-factly.

“If I say yes,” Rodney started to say slowly, “and you become my mate, will you agree to the rest of my terms?”

“I think you have it wrong,” John said as he tilted his head, “You will become _my_ mate, as I am the Alph-” Rodney cut him off by biting into his neck at his jugular; John gulped as he mumbled, “Your mate...”

Rodney released his throat and glared at him as he growled, “Answer my question!”

“What are your terms?”

“You’re honestly thinking of saying no to me?” Rodney demanded incredulous, “I was serious when I said you’d die if you refuse to become my mate; Ronon will take you back to the warehouse, drain you of blood, chop you up into little pieces, marinate you in acid for a few days and then dump you somewhere obscure. Does that really sound preferable to becoming my mate?”

“I don’t even know who you are,” John said, moaning out the last two words as Rodney sat up.

“That’s even better; it’ll give us something to talk about. Now,” the Omega said as he rested his hands on the Alpha’s chest, fingers brushing lightly over the pebbled nipples, “I’m getting tired of ignoring my body’s needs; if you don’t bite me I’ll have your answer.” And with that said the Omega pushed up slowly, eliciting moans from them both, before dropping down and rolling his hips.

Rodney kept the pace slow as he rode John, wanting to enjoy having sex in his own bed if it was to be the last, until he could no longer ignore his body’s demand to climax. Fumbling a hand out as he pushed up, he grabbed the remote control and released John’s restraints as he quickened the pace; John immediately brought his hands to the Omega’s hips and thrust into him, burying his knot in Rodney as he bit down into his flesh. When John’s teeth pierced skin, drawing blood, it tipped Rodney over the edge and he roared as he climaxed, his vision whiting out.

When Rodney was once again aware of his surroundings they were laying on the sides; John had an arm tucked under his head and was grinning at him, “I think you fainted.”

Rodney rolled his eyes as he made himself comfortable, his shoulder throbbed where John had bit him and his body thrummed in contentment at being knotted, “I passed out after a truly spectacular orgasm, I did not faint!”

“So,” John said rubbing at his neck as he glanced at Rodney’s shoulder, “I guess we’re mates now.”

“Yes . . . why’d you do it?” Rodney found himself asking, curiosity piqued, “You could have killed me while we were knotted, and climbed out of the window or something…”

“You have Ronon staying the night,” John said as he avoided eye contact, “he would probably just have hunted me down and killed me.”

Rodney narrowed his eyes as he gazed at the Alpha, “You’re keeping something from me!”

Sighing, John brought up a hand to cup the Omega’s cheek, “You have really beautiful blue eyes Rodney McKay, and a sweet scent even with the Beta pheromones you cover yourself with.”

“You said you didn’t know who I was,” Rodney protested as he tried to pull away, heart racing.

“Calm down McKay,” John snapped, “Anybody that reads a newspaper, or watches the news, knows your name; that doesn’t mean that they know _you_.”

“Oh,” Rodney said as he moved closer to John, “okay then. So, what do you want to know?”

John huffed a laugh as he pushed up onto an elbow, “I’ve been kidnapped, hauled around in a truck, drugged, washed, tied to your bed and almost raped-”

“Hey,” Rodney protested, earning himself a glare.

“Forced to bond with you and _now_ you want to get to know me?” John shook his head in disbelief, tugging on Rodney’s arm, “Come one, move up. I want to sleep, then eat, and then freak the fuck out because really McKay, you’re kinda fucked up.” John dropped down onto a pillow, eyes falling closed as he snuggled into it. “Sheet, blanket, something . . . cover us up McKay and get some sleep; who knows, I might change my mind come daylight.”

Rodney chewed on his bottom lip, for the first time unsure of his actions, until John’s hand smacked into his shoulder as the younger man whined his name. “How the hell am I supposed to get a blanket if we’re tied together?” 

“Figurrit out,” came the mumbled answer.

In the old end Rodney shoved John onto his back and covered the Alpha with his body, causing a pleased sound from the other man and a jerk of his hips as he came a second time. Burying his nose in John’s neck, Rodney decided to worry later about what he’d done, and fell asleep to the comforting scent of his Alpha.


	2. Chapter 2

**Notes for the Chapter:**

> So this will probably have more chapters? Not sure where to go next though... but I'm sure it'll come to me!
> 
> Oh and for those following my 'The Way to a Man's Heart' series, I have completed it with ['Midnight Snack'](http://archiveofourown.org/works/2364098) but the fic isn't showing on the site properly :( so I made the title a link!

“What,” Rodney demanded angrily as something kept poking him in the shoulder, swinging his arm in that direction without opening his eyes.

“Got that report you wanted,” Ronon rumbled.

“Big guy,” Rodney grumbled, “couldn’t this wait till after breakfast or something? I was really hoping to get knotted again this morning.”

“You’re gonna want to see what the report has to say,” came the distant voice of Elizabeth Weir, one of his right-hand women.

“Fine,” he muttered as he sat up slowly, enjoying the way his body ached at the movement. When he was leaning back against the bedframe he opened his eyes to find Ronon sitting on John, as he held a tablet out at him. “Get off of him you Neanderthal!” he yelled pushing at the other man, but Ronon continued to ignore him as he stared down at the other Alpha.

The tablet was thrust at him as the other man spoke, “Just read the report.”

Taking the tablet, Rodney groused about the other man under his breath as he started to read the report he’d had compiled on the Alpha he was now bonded to, not making it beyond his full name before snapping out, “Get rid of him Ronon!”

“What!” John exclaimed as he was hauled out of the bed, “Rodney what the hell-” he managed to shout before he was rendered unconscious by Ronon.

“Maybe you should send his _father_ ,” Rodney spat out angrily as he climbed out of the bed, “a piece of him as a warning.” 

Ronon grunted in answer as he wrapped the other Alpha in a sheet before tossing him over his shoulder and carrying him from the room, Elizabeth following him out.

Hurling the tablet at the nearest wall in anger, Rodney stalked into his personal bathroom to hopefully scrub the other man’s claim from him. The anger still bubbling, he threw a fist at the mirror and watched in satisfaction as it shattered and fell to pieces, until the pain in his fist broke through. He strode out into his bedroom again as he cradled his hand to him, making his way to the intercom which stood on his desk; jabbing a finger at the button for Miko he demanded that she send Carson up to his room as soon as he arrived.

A quick check of his fist showed no glass was embedded there, and so headed into the bathroom again for his badly needed shower.

-

Half an hour later found Rodney having breakfast with four of his closest friends, but as they chatted amongst themselves he sulked at his end of the table. Most mornings he ate voraciously as he chatted away about his plans for his empire but today he could barely concentrating on the food before him. It was almost a relief when the phone in the middle of the table rang and Teyla answered it, but that relief soon fled when he heard Ronon on the other side of the line.

“It is Ronon,” she stated to him unnecessarily, “he wishes to be put on speakerphone.” 

Rodney really didn’t want to know what the other man had to say if it had to do with John, but that might not be the reason for the call so he nodded.

After pressing the correct button she spoke into the machine’s mic, “Go ahead Ronon.”

_“Morning,” his head of security rumbled, “it’s about Sheppard. He woke up on the way back to the warehouse; started yelling about someone named Lorne until I made him shut up, said somethin’ about being at the dive lookin’ for his friend when he got taken. Might be lying to get outta dyin’, might be tellin’ the truth, either way thought you’d want to know.”_

Rodney’s first urge was to say that he didn’t care, despite the fact that he did, and that Ronon should follow the orders given to him, but a look around the table stopped him. Elizabeth had pulled her tablet closer at the mention of the name Lorne and was now typing furiously at it, muttering about it sounding familiar while Teyla typed equally as furious at her own tablet.

“Put him in one of the holding cells,” Rodney commanded, “and get his full story; it’ll be easy to look into and if he’s lying, you kill him.”

A grunt was heard before the call was cut off.

“Elizabeth, Teyla, one of you want to tell me what’s going on?”

“Why the fuck do you smell like a bonded Omega Mer?” came the angry growl of Jeannie Miller as she prowled into the room.

“Jeannie please,” Rodney sighed, “now is not the time.”

“Oh yes it most definitely is,” she stated firmly as she fixed the other Alphas in the room with a glare, growling out her next question, “which one of you claimed my brother?”

The other Alphas had the good sense to avoid eye contact with the irate female as she advanced on the table. 

“Oh for goodness sake Jean,” Rodney yelled as he stood, “it wasn’t any of them, and it wasn’t Ronon either; they know better than to piss you off.”

“Well then who the fuck was it?” she demanded as she turned to glare at him.

But before he could answer the phone rang again, this time it was the internal ring, and when Radek answered it was to Miko saying that Patrick Sheppard was on hold to speak to Rodney; with a resigned sigh he told her to put it through. Jeannie pulled out a chair and sat down facing him, glare still in place.

“Patrick Sheppard, how nice of you to call,” Rodney greeted sarcastically.

_“McKay, I’ll get straight to the point,” the other man said in a clipped tone, “I want my son back!”_

“Well maybe you shouldn’t have tried using him in this game you will ultimately lose!” Rodney spat out.

_“What?!? I would never!” the other man spluttered and after taking a few breaths he continued, “Just . . . give me back my son McKay; John has no part in this.”_

“So if you didn’t send him in to infiltrate my organisation,” Rodney said doubtfully, “how do you know I have him?”

_There was a long moment of silence from the other side until Patrick Sheppard responded, voice tight, “My mole informed me that you have him…”_

“Thank you for confirming my suspicions Patrick,” Rodney said almost gleefully, “expect to receive your mole’s remains in the next few days.”

_“But what about Jo-”_

The rest of what Patrick Sheppard said was cut off by Rodney ending the call. 

“Get Ronon on the line,” he ordered as he leaned back into his seat, needing to think.

“Rodney,” Teyla started to say in her most soothing tones at the same time that Jeannie growled out his name.

“Yes what?” Rodney demanded impatiently.

Teyla allowed his sister to speak first, “Why the hell do you have John Sheppard? And is he the Alpha that claimed you?”

“To your second question, yes,” he sighed as he rubbed at his forehead, the day had barely begun and already he was getting a tension headache. “As for your first question, that is too complicated to answer right now. Teyla?” he said, motioning for her to speak.

“We processed one Evan Lorne last month,” Elizabeth said as she transferred the information on her tablet to one of the screens that circled the table. 

“He was picked up by Michael at the same dive bar that John was,” Teyla added as she transferred John’s file to another screen, “and according to the missing file opened by law enforcement, John Sheppard was the one to report him missing.”

“So you’re thinking that he got picked up looking for this Lawn person?” Rodney questioned, “That this isn’t part of Patrick Sheppard’s plan to overthrow me?”

_At that moment Ronon’s voice filled the room, “You called?”_

“Patrick Sheppard admitted that he has a mole in our organisation, find it and exterminate it please,” Rodney informed him.

_“Will do,” Ronon said and then cut the call._

“I want a full background on both John and this Lawn person Teyla,” Rodney said as he rubbed absentmindedly at the bite mark in his neck. “Radek, Carson; you both have work to do, so please go and do it. Elizabeth you’ll have to cover for me until the bonding scent fades, and I ascertain that my Beta camo scent is still effective; tell them I’m taking a sabbatical but still keeping an eye on the business. I want full reports tonight at supper!”

As the three Alphas filed from the room the phone rang, Rodney answered it himself by demanding, “What?” despite it being an external call.

_“I found the mole,” Ronon replied casually._

“You’ve barely had time to register my words,” Rodney snapped irritably.

_“It’s Ford,” came the unperturbed reply, “wanted him to take over from me with Sheppard. Your Alpha lit up the moment he saw him, called him by name so I got him in one of the other cells.”_

“Dammit,” Rodney sighed, “and he had such potential . . . leave them for later, I need to think about it.”

_“Right,” the Alpha said, “need me for anything?”_

Rodney was about to reply in the negative when he noticed Teyla nodding at him. “Come back to the house,” he ordered.

There was no response this time before the call was ended.

“What now?” Rodney asked tiredly, at this rate he would have to take a nap in order to get through the day.

“It would seem that John and Evan Lorne have been best friends for years,” Teyla stated, pointedly ignoring his remark of “How sweet” as she continued, “they are currently sharing an apartment and have both enlisted for the United States Air Force.”

“A fly boy,” he muttered under his breath before asking her, “So why do we need Ronon?”

“Evan Lorne was picked up by Acastus Kolya the day after he was processed,” she said as she looked at him with her earnest eyes, “and he is still alive, despite being forced into the fighting ring 19 times already.”

“How is it that you are so good at your job Teyla, when you have such a soft heart,” he asked rhetorically. “Message Kolya, tell him I want Lawn, pay him whatever he wants, then go with Ronon to retrieve him.”

Teyla smiled beautifully as she turned back to her tablet, “I knew you would see the merit of freeing your new Alpha’s best friend Rodney.”

“What are you going to do about your Alpha dear brother?” Jeannie asked sweetly, she had moved to sit beside him as he and Teyla had been talking, and now rested her hand on his forearm to keep him in place.

Rodney sighed for what felt like the hundredth time that day, “I have no idea.”

**Author's Note:**

> Right, so I actually wrote that . . . let me know what you think with a comment?


End file.
